Depending on how jobs are submitted to cluster-managing executors (pbspro, slurm, etc), it may be required to add clusterOptions '-V' to pass environment variables to process blocks that get submitted as independent jobs on the queue. For PBS Pro, the '-V' parameter flags that all environment variables from the submitting environment get passed to the child process that gets submitted. The analogous sbatch command argument is '--export=All'.
If required, changes needs to happen within the nextflow pipeline codes (not in the config files); e.g. the all-by-all blast block in EST needs to have a clusterOptions '-V' line added in the process' preamble space. Currently, this will be left as a "Note" issue to remind ourselves what may be required in certain instances. It is an executor-specific change after all.
Depending on how jobs are submitted to cluster-managing executors (pbspro, slurm, etc), it may be required to add
clusterOptions '-V'to pass environment variables to process blocks that get submitted as independent jobs on the queue. For PBS Pro, the'-V'parameter flags that all environment variables from the submitting environment get passed to the child process that gets submitted. The analogous sbatch command argument is'--export=All'.If required, changes needs to happen within the nextflow pipeline codes (not in the config files); e.g. the all-by-all blast block in EST needs to have a
clusterOptions '-V'line added in the process' preamble space. Currently, this will be left as a "Note" issue to remind ourselves what may be required in certain instances. It is an executor-specific change after all.